I would do a couple of things. Unless you have surgically repaired shoulders with minimal range of motion, you inability to hold the bar for squats would concern me. I would work on shoulder flexibility. Where you trying high bar or low bar squats? Bar position can affect shoulder flex too.

I love front squats. There are also zercher squats and BB hack squats. All of these are good alternatives but with limitations. Fronts and zercher can not carry the weight of back squats but activate the muscles in much the same way. Hacks hit the legs a bit differently, but you can use as much weight as you can hold at arms length behind you.